Hello Thomas,
actually the workflow that you have figured out is the one that I would recommend. You should primarily stay with the FLAIR file and let it create the .inp accordingly.
Actually, if you have “variations” of your input you might want to use the possibility of having one project under which you spawn child simulations that are different only in details that you can define. For example you can vary the energy or any other parameter by setting it to a variable in the FLAIR input and in the run tab of FLAIR you can then set the values that should be used for this variable. Have a look at the following slides:
FLAIR-runtab.pdf (1.5 MB)
Hope that helps
Chris